RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16850
(174 letters)
>2bwn_A 5-aminolevulinate synthase; tetrapyrrole biosynthesis, heme
biosynthesis, pyridoxal PHOS dependent, transferase,
acyltransferase; HET: LLP; 2.1A {Rhodobacter capsulatus}
SCOP: c.67.1.4 PDB: 2bwo_A* 2bwp_A*
Length = 401
Score = 185 bits (471), Expect = 5e-58
Identities = 60/129 (46%), Positives = 79/129 (61%), Gaps = 2/129 (1%)
Query: 11 YEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAA--YEYTDSEKEVTVYCSNDYLGMSCH 68
Y + I K + YR F + R FP A ++++TV+C NDYLGM H
Sbjct: 3 YNLALDKAIQKLHDEGRYRTFIDIEREKGAFPKAQWNRPDGGKQDITVWCGNDYLGMGQH 62
Query: 69 PKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDST 128
P V +A+ EALE G G+GGTRNISG + +H +LE ++A LHQKEA LVF+S Y AND+T
Sbjct: 63 PVVLAAMHEALEAVGAGSGGTRNISGTTAYHRRLEAEIAGLHQKEAALVFSSAYNANDAT 122
Query: 129 LFTLGKMIP 137
L TL + P
Sbjct: 123 LSTLRVLFP 131
>3kki_A CAI-1 autoinducer synthase; quorum sensing, CQSA, P virulence,
acyltransferase, aminotransferase, pyridoxal PHO
transferase; HET: PLP; 1.80A {Vibrio cholerae} PDB:
3hqt_A* 2wk9_A* 2wk8_A* 2wka_A* 2wk7_A
Length = 409
Score = 141 bits (358), Expect = 3e-41
Identities = 22/118 (18%), Positives = 50/118 (42%), Gaps = 3/118 (2%)
Query: 17 EQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPKVKSAVR 76
++ K DH + +N+ + + + + SNDYL ++ HP +K+ +
Sbjct: 27 PDFIQNKIDHYIENYFDINKNGKHLVLG---KQASPDDIILQSNDYLALANHPLIKARLA 83
Query: 77 EALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLFTLGK 134
++L + + + N +E+ +A+ + L+ S + AN L T+ +
Sbjct: 84 KSLLEEQQSLFMSASFLQNDYDKPMIEKRLAKFTGFDECLLSQSGWNANVGLLQTICQ 141
>2w8t_A SPT, serine palmitoyltransferase; HET: LLP; 1.25A {Sphingomonas
paucimobilis} PDB: 2w8u_A* 2w8w_A* 2xbn_A* 2w8j_A*
2w8v_A* 2jg2_A* 2jgt_A 2x8u_A*
Length = 427
Score = 138 bits (350), Expect = 7e-40
Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 3/130 (2%)
Query: 3 TTMREPFPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDY 62
R+ D + K F V + A K+ + + +Y
Sbjct: 18 APERDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEA---VIRGKDTILLGTYNY 74
Query: 63 LGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCY 122
+GM+ P V +A +EALEKFG+G G+R ++G H ++E+ + + +VF++ Y
Sbjct: 75 MGMTFDPDVIAAGKEALEKFGSGTCGSRMLNGTFHDHMEVEQALRDFYGTTGAIVFSTGY 134
Query: 123 VANDSTLFTL 132
+AN + TL
Sbjct: 135 MANLGIISTL 144
>3tqx_A 2-amino-3-ketobutyrate coenzyme A ligase; energy metabolism,
transferase; HET: PLP; 2.30A {Coxiella burnetii}
Length = 399
Score = 130 bits (328), Expect = 7e-37
Identities = 32/122 (26%), Positives = 60/122 (49%), Gaps = 5/122 (4%)
Query: 11 YEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPK 70
+++I K+ Y+ + + P E EKEV +C+N+YLG++ HP
Sbjct: 7 ILSQLNKEIEGLKKAGLYKSERIITS-----PQNAEIKVGEKEVLNFCANNYLGLADHPA 61
Query: 71 VKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLF 130
+ + +E++G G R I G H++LE+D++ + ++++SC+ AN
Sbjct: 62 LIKTAQTVVEQYGFGMASVRFICGTQTIHKELEKDISEFLGTDDTILYSSCFDANGGLFE 121
Query: 131 TL 132
TL
Sbjct: 122 TL 123
>1bs0_A Protein (8-amino-7-oxonanoate synthase); PLP-dependent acyl-COA
synthase, biotin biosynthesis, 8-AMIN oxonanoate
synthase; 1.65A {Escherichia coli} SCOP: c.67.1.4 PDB:
2g6w_A* 1dje_A* 1dj9_A*
Length = 384
Score = 126 bits (318), Expect = 2e-35
Identities = 32/122 (26%), Positives = 64/122 (52%), Gaps = 5/122 (4%)
Query: 11 YEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPK 70
+++ + + ++ + R V + A +++ + SNDYLG+S HP+
Sbjct: 3 WQEKINAALDARRAADALRRRYPVAQ-----GAGRWLVADDRQYLNFSSNDYLGLSHHPQ 57
Query: 71 VKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLF 130
+ A ++ E+FG G+GG+ ++SG S+ H+ LEE++A L+F S + AN + +
Sbjct: 58 IIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIA 117
Query: 131 TL 132
+
Sbjct: 118 AM 119
>1fc4_A 2-amino-3-ketobutyrate conenzyme A ligase; 2-amino-3-ketobutyrate
COA ligase, pyridoxal phosphate, COEN transferase,
structural genomics; HET: PLP; 2.00A {Escherichia coli}
SCOP: c.67.1.4
Length = 401
Score = 119 bits (301), Expect = 8e-33
Identities = 31/129 (24%), Positives = 57/129 (44%), Gaps = 6/129 (4%)
Query: 4 TMREPFPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYL 63
MR F + + + ++ R+ T+ A V +C+N+YL
Sbjct: 3 HMRGEF--YQQLTNDLETARAEGLFKEE----RIITSAQQADITVADGSHVINFCANNYL 56
Query: 64 GMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYV 123
G++ HP + +A + ++ G G R I G H++LE+ +A E ++++SC+
Sbjct: 57 GLANHPDLIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFD 116
Query: 124 ANDSTLFTL 132
AN TL
Sbjct: 117 ANGGLFETL 125
>3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold type
I, acyltransferase, PY phosphate; HET: PLP; 2.30A
{Sphingobacterium multivorum}
Length = 398
Score = 109 bits (276), Expect = 3e-29
Identities = 32/116 (27%), Positives = 59/116 (50%), Gaps = 5/116 (4%)
Query: 17 EQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPKVKSAVR 76
+ + + K Y F+ + E + V ++ SN YLG++ ++ A +
Sbjct: 13 KIVEELKAKGLYAYFRPIQS-----KQDTEVKIDGRRVLMFGSNSYLGLTTDTRIIKAAQ 67
Query: 77 EALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTLFTL 132
+ALEK+GTG G+R ++G H +LEE ++ KEA ++F++ + +N L L
Sbjct: 68 DALEKYGTGCAGSRFLNGTLDIHVELEEKLSAYVGKEAAILFSTGFQSNLGPLSCL 123
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 50.4 bits (120), Expect = 6e-08
Identities = 35/192 (18%), Positives = 65/192 (33%), Gaps = 49/192 (25%)
Query: 8 PFPYEDFFHEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGM-- 65
P FF ++++ F K+ T AA + + E+ +LG
Sbjct: 21 LVPTASFFIASQLQEQ-------FNKILPEPTEGFAADDEPTTPAELVG----KFLGYVS 69
Query: 66 -SCHPKVKSAVRE----ALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLV--F 118
P + L +F +I ++L + L+E+ L + + +
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI--HALAAKLLQENDTTLVKTKELIKNYI 127
Query: 119 TSCYVAN------------------DSTLFTL----GKMIPYFTEL--IY-FYRFLANTT 153
T+ +A ++ L + G YF EL +Y Y L
Sbjct: 128 TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV--G 185
Query: 154 DIIKEASKELQE 165
D+IK +++ L E
Sbjct: 186 DLIKFSAETLSE 197
Score = 33.1 bits (75), Expect = 0.044
Identities = 34/174 (19%), Positives = 54/174 (31%), Gaps = 63/174 (36%)
Query: 5 MREPFPYEDFFHEQIMKKKRDHSYRVFKKVNR-------------L-ATNF--PA--AYE 46
+RE Y E + + + ++FK++N L AT F PA E
Sbjct: 1684 IREN--YSAMIFET-IVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 47 YTDSE--KEVTVYCSNDY-----LG-----------MSCHPKVKSAVR----------EA 78
E K + ++ LG MS ++S V A
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMS----IESLVEVVFYRGMTMQVA 1796
Query: 79 LEKFGTGAGGTRNISGN------SLFHEKLEEDVARLHQKEAGLVFTSCYVAND 126
+ + G I+ N S E L+ V R+ K G + + N
Sbjct: 1797 VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERV-GKRTGWL---VEIVNY 1846
Score = 31.6 bits (71), Expect = 0.14
Identities = 29/197 (14%), Positives = 56/197 (28%), Gaps = 49/197 (24%)
Query: 16 HEQIMKKKRDHSYRVFKKV-NRLATNFPAAYEYTDSE------KEVTVYCS--------N 60
EQ M + + + V NR +F Y ++ + +T++
Sbjct: 1627 QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRE 1686
Query: 61 DYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFH--EKLEE-----------DVA 107
+Y M V ++ + F + + + L + A
Sbjct: 1687 NYSAMIFETIVDGKLK-TEKIF---KEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA 1742
Query: 108 RLHQ-KEAGLVFTSCYVANDSTLFTLG---------KMIPYFTELIY--FYRFLANTTDI 155
K GL+ A S LG ++ L+ FYR + +
Sbjct: 1743 AFEDLKSKGLIPADATFAGHS----LGEYAALASLADVMS-IESLVEVVFYRGMTMQVAV 1797
Query: 156 IKEASKELQEDMIDLTP 172
++ MI + P
Sbjct: 1798 PRDELGRSNYGMIAINP 1814
>2eo5_A 419AA long hypothetical aminotransferase; PLP enzyme, structural
genomics, NPPSFA, N project on protein structural and
functional analyses; HET: PLP; 1.90A {Sulfolobus
tokodaii}
Length = 419
Score = 33.3 bits (77), Expect = 0.029
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 63 LGMSCHPKVKSAVREALEKF 82
LG HP+V E ++K
Sbjct: 56 LGWPSHPEVIKIGIEQMQKL 75
>1sff_A 4-aminobutyrate aminotransferase; enzyme complexes; HET: IK2;
1.90A {Escherichia coli} SCOP: c.67.1.4 PDB: 1sf2_A*
1szk_A* 1szu_A* 1szs_A*
Length = 426
Score = 30.2 bits (69), Expect = 0.32
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 67 CHPKVKSAVREALEKF 82
HPKV +AV L+K
Sbjct: 58 LHPKVVAAVEAQLKKL 73
>3dxv_A Alpha-amino-epsilon-caprolactam racemase; fold-TYPE1,
pyridoxal-5'-phosphate dependent racemase, pyrid
phosphate, isomerase; HET: PLP; 2.21A {Achromobacter
obae} PDB: 2zuk_A* 3dxw_A*
Length = 439
Score = 30.2 bits (69), Expect = 0.33
Identities = 5/16 (31%), Positives = 7/16 (43%)
Query: 67 CHPKVKSAVREALEKF 82
HP + +AV A
Sbjct: 60 GHPAIVAAVSAAAANP 75
>3oks_A 4-aminobutyrate transaminase; ssgcid, transferase, seattle
structural genomics center for infectious disease; HET:
LLP; 1.80A {Mycobacterium smegmatis} PDB: 3r4t_A*
3q8n_A
Length = 451
Score = 29.9 bits (68), Expect = 0.40
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 67 CHPKVKSAVREALEKF 82
PKV AVR + F
Sbjct: 78 SAPKVVEAVRSQVGDF 93
>4ffc_A 4-aminobutyrate aminotransferase (GABT); structural genomics,
niaid, national institute of allergy AN infectious
diseases; HET: LLP; 1.80A {Mycobacterium abscessus}
Length = 453
Score = 29.9 bits (68), Expect = 0.42
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 67 CHPKVKSAVREALEKF 82
HP V +A+ + F
Sbjct: 81 SHPAVAAAIADQATHF 96
>1zod_A DGD, 2,2-dialkylglycine decarboxylase; pyridoxal, cesium, lyase;
HET: MES PLP; 1.80A {Burkholderia cepacia} SCOP:
c.67.1.4 PDB: 1dka_A* 1m0o_A* 1m0p_A* 1m0n_A* 1zc9_A*
1zob_A* 1m0q_A* 2dkb_A* 1dgd_A* 1dge_A* 1d7u_A* 1d7s_A*
1d7r_A* 1d7v_A* 1z3z_A*
Length = 433
Score = 29.1 bits (66), Expect = 0.76
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 67 CHPKVKSAVREALEKF 82
CHP++ S + E K
Sbjct: 60 CHPEIVSVIGEYAGKL 75
>3tnd_B Antitoxin VAPB; PIN domain, spovt/ABRB-like domain, ribonuclease,
DNA-bindin translation; 2.70A {Shigella flexneri}
Length = 81
Score = 27.5 bits (61), Expect = 0.84
Identities = 10/51 (19%), Positives = 15/51 (29%)
Query: 20 MKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPK 70
M H VF A P A ++ K V V ++ +
Sbjct: 1 MHHHHHHETTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGE 51
>1jg8_A L-ALLO-threonine aldolase; glycine biosynthesis, pyridoxal-5'-
phosphate, calcium binding site, structural genomics,
PSI; HET: LLP; 1.80A {Thermotoga maritima} SCOP:
c.67.1.1 PDB: 1lw4_A* 1lw5_A* 1m6s_A* 2fm1_A*
Length = 347
Score = 28.0 bits (63), Expect = 1.4
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 101 KLEEDVARLHQKEAGLVFTSCYVAN 125
+LE A KEA L S + N
Sbjct: 42 ELERLAAETFGKEAALFVPSGTMGN 66
>3pj0_A LMO0305 protein; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-biology,
lyase; HET: LLP MSE; 1.80A {Listeria monocytogenes}
Length = 359
Score = 28.1 bits (63), Expect = 1.5
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 101 KLEEDVARLHQKEAGLVFTSCYVAN 125
E +A++ K++ + F S +A
Sbjct: 52 DFETKIAKILGKQSAVFFPSGTMAQ 76
>3lws_A Aromatic amino acid beta-eliminating lyase/threonine aldolase;
structural genomics, joint center for structural
genomics, JCSG; HET: LLP MSE; 2.00A {Exiguobacterium
sibiricum}
Length = 357
Score = 28.1 bits (63), Expect = 1.5
Identities = 5/25 (20%), Positives = 10/25 (40%)
Query: 101 KLEEDVARLHQKEAGLVFTSCYVAN 125
E+ A + + + F S +A
Sbjct: 51 PFEQKFADVLGMDDAVFFPSGTMAQ 75
>2epj_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA,
structural genomics, NPPSFA; HET: PMP; 1.70A {Aeropyrum
pernix} PDB: 2zsl_A* 2zsm_A*
Length = 434
Score = 27.9 bits (63), Expect = 2.1
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP+V AV EAL + +G
Sbjct: 73 KHPRVLEAVEEALARGWLYGA 93
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.9 bits (61), Expect = 2.3
Identities = 24/207 (11%), Positives = 53/207 (25%), Gaps = 52/207 (25%)
Query: 2 DTTMREPFPYEDFF--------HEQIMKKKRDHSYRVFKKVNRLATNFPAAYEYTDSEKE 53
++ ++ F+ E +++ + Y++ + + S +
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 54 VTVYCSNDYLGMSCHPK-------VKSAVREALEKFG-------TGAGGTRN------IS 93
L + V++A +A F T TR +S
Sbjct: 233 E----LRRLLKSKPYENCLLVLLNVQNA--KAWNAFNLSCKILLT----TRFKQVTDFLS 282
Query: 94 GNSLFHEKLEEDVARLHQKEAGLVFTSCYVANDSTL---------FTL---GKMIPYFTE 141
+ H L+ L E + L L + I
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342
Query: 142 LIYFYRFLAN--TTDIIKEASKELQED 166
++ + T II+ + L+
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPA 369
Score = 27.5 bits (60), Expect = 2.8
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 17/57 (29%)
Query: 98 FHEKLEEDVARLHQKEAGLV----FTSCYVANDSTLFTLGKMIPYFTELIYFYRFLA 150
KLE + A LH+ +V + ++D L + YFY +
Sbjct: 435 LKVKLENEYA-LHRS---IVDHYNIPKTFDSDDLIPPYLDQ---------YFYSHIG 478
>2yky_A Beta-transaminase; transferase; HET: PLP SFE; 1.69A {Mesorhizobium
SP} PDB: 2ykv_A* 2yku_A* 2ykx_A*
Length = 465
Score = 27.6 bits (62), Expect = 2.3
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP +++AV AL T
Sbjct: 117 SHPVIRAAVERALAVGLNLST 137
>3l44_A Glutamate-1-semialdehyde 2,1-aminomutase 1; alpha beta class,
PLP-dependent transferase-like, bacillus A csgid,
porphyrin biosynthesis; HET: LLP; 2.05A {Bacillus
anthracis}
Length = 434
Score = 27.5 bits (62), Expect = 2.4
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP + A+ A E +GT
Sbjct: 72 AHPHITKAITTAAENGVLYGT 92
>3k28_A Glutamate-1-semialdehyde 2,1-aminomutase 2; biosynthesis of
cofactors, prosthetic groups, and carriers, csgid,
cytoplasm, isomerase; HET: MSE PLP; 1.95A {Bacillus
anthracis str} PDB: 3bs8_A*
Length = 429
Score = 27.5 bits (62), Expect = 2.6
Identities = 5/21 (23%), Positives = 10/21 (47%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
+ +V A++ E+ FG
Sbjct: 70 ANDRVVEALKAVAERGTSFGA 90
>3fq8_A Glutamate-1-semialdehyde 2,1-aminomutase; drug resistance,
microev0lution, integrated approach, chlorophyll
biosynthesis; HET: PMP; 2.00A {Synechococcus elongatus
pcc 6301} PDB: 2hp1_A* 2hoz_A* 2hoy_A* 2hp2_A* 3fq7_A*
2gsa_A* 3gsb_A* 4gsa_A* 3fqa_A* 2cfb_A*
Length = 427
Score = 27.4 bits (62), Expect = 2.7
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP+V A++ A+EK FG
Sbjct: 69 AHPEVIEALKVAMEKGTSFGA 89
>2e7u_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA,
structural genomics, NPPSFA; HET: PMP; 1.90A {Thermus
thermophilus}
Length = 424
Score = 27.5 bits (62), Expect = 2.7
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HPKV + VRE LE+ FG
Sbjct: 69 AHPKVLARVRETLERGLTFGA 89
>2cy8_A D-phgat, D-phenylglycine aminotransferase; structural genomics,
NPPSFA, national PROJ protein structural and functional
analyses; 2.30A {Pseudomonas stutzeri}
Length = 453
Score = 27.2 bits (61), Expect = 2.8
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP+V +A+ EAL +
Sbjct: 74 GHPRVNAAIAEALSHGVQYAA 94
>4e77_A Glutamate-1-semialdehyde 2,1-aminomutase; structural genomics,
center for structural genomics of infec diseases,
csgid, porphyrin biosynthesis; 2.00A {Yersinia pestis}
Length = 429
Score = 27.5 bits (62), Expect = 2.9
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 67 CHPKVKSAVREALEK---FGT 84
HP ++ AV EA+E+ FG
Sbjct: 70 NHPAIRQAVIEAVERGLSFGA 90
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 26.8 bits (60), Expect = 3.2
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 22 KKRDHSYRVFKKVNRLA 38
+ +DHS +V KK+ R A
Sbjct: 88 RPQDHSQKVNKKMYRGA 104
>1ohv_A 4-aminobutyrate aminotransferase; PLP-dependent enzyme, 4- AMIN
acid, antiepileptic drug target; HET: PLP; 2.3A {Sus
scrofa} SCOP: c.67.1.4 PDB: 1ohw_A* 1ohy_A*
Length = 472
Score = 26.9 bits (60), Expect = 3.6
Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 1/57 (1%)
Query: 63 LGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFT 119
+G HP + V++ I F EKL E + + K + T
Sbjct: 77 IGY-SHPALVKLVQQPQNVSTFINRPALGILPPENFVEKLRESLLSVAPKGMSQLIT 132
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 26.8 bits (60), Expect = 3.8
Identities = 5/17 (29%), Positives = 10/17 (58%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K R + Y + ++V +L
Sbjct: 87 KPRSYDYTLPRQVRQLG 103
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 26.7 bits (59), Expect = 4.0
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD + ++ KK RLA
Sbjct: 144 KPRDWTIKMNKKERRLA 160
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 26.5 bits (59), Expect = 4.2
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD+SY + KKV +
Sbjct: 93 KPRDYSYTLPKKVRKKG 109
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 26.6 bits (59), Expect = 4.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 22 KKRDHSYRVFKKVNRLA 38
K RD S ++ KK+ +LA
Sbjct: 92 KPRDWSKKLNKKMKKLA 108
>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus,
hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A
Length = 677
Score = 26.8 bits (58), Expect = 4.5
Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 2/77 (2%)
Query: 18 QIMKKKRDHSYRVFKKVNRL--ATNFPAAYEYTDSEKEVTVYCSNDYLGMSCHPKVKSAV 75
+ ++ L T A ++ D + + D +GM + ++ +
Sbjct: 335 SVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRII 394
Query: 76 REALEKFGTGAGGTRNI 92
+L K G R +
Sbjct: 395 FYSLIKPSINEKGEREL 411
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
ribosomal protein L3; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_D
Length = 175
Score = 26.1 bits (58), Expect = 4.7
Identities = 4/18 (22%), Positives = 7/18 (38%)
Query: 21 KKKRDHSYRVFKKVNRLA 38
+ + Y + KV L
Sbjct: 60 RGPTSYYYMLPMKVRALG 77
>3ek6_A Uridylate kinase; UMPK unique GTP B site, allosteric regulation,
ATP-binding, nucleotid binding, pyrimidine biosynthesis,
transferase; 2.34A {Xanthomonas campestris PV} PDB:
3ek5_A
Length = 243
Score = 26.0 bits (57), Expect = 7.0
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 4/80 (5%)
Query: 61 DYLGMSCHPKVKSAVREALEKFGTGAGGTRNISGNSLFHEKLEEDVARLHQKEAGLVFTS 120
D++GM A+++ALEK G I N + + + R +K +F +
Sbjct: 77 DHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAA 136
Query: 121 C----YVANDSTLFTLGKMI 136
+ DS I
Sbjct: 137 GTGNPFFTTDSGAALRAIEI 156
>1pff_A Methionine gamma-lyase; homocysteine; 2.50A {Trichomonas vaginalis}
SCOP: c.67.1.3
Length = 331
Score = 25.9 bits (58), Expect = 7.1
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 102 LEEDVARLHQKEAGLVFTSCYVANDSTLFTL 132
LE +A+L EA S A ++++T
Sbjct: 3 LEGKIAKLEHAEACAATASGMGAIAASVWTF 33
>1q6h_A FKBP-type peptidyl-prolyl CIS-trans isomerase FKP; chaperone,
peptidyl-prolyl isomerase, heat shock protein, FK
family; HET: MSE; 1.97A {Escherichia coli} SCOP:
d.26.1.1 PDB: 1q6i_A* 1q6u_A
Length = 224
Score = 25.9 bits (57), Expect = 7.2
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 103 EEDVARLHQKEA---GLVFTSCYVANDSTLFTLGKMIPYFTE 141
+ D ++ K G F + Y + F L +IP +TE
Sbjct: 138 DSDTVVVNYKGTLIDGKEFDNSYTRGEPLSFRLDGVIPGWTE 179
>1qgn_A Protein (cystathionine gamma-synthase); methionine biosynthesis,
pyridoxal 5'-phosphate, gamma-famil; HET: PLP; 2.90A
{Nicotiana tabacum} SCOP: c.67.1.3 PDB: 1i41_A* 1i48_A*
1i43_A*
Length = 445
Score = 26.1 bits (58), Expect = 7.5
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 102 LEEDVARLHQKEAGLVFTSCYVANDSTLFTL 132
LEE ++ L E+ L+ S A+ L L
Sbjct: 119 LEEKISALEGAESTLLMASGMCASTVMLLAL 149
>3i16_A Aluminum resistance protein; YP_878183.1, carbon-sulfur lyase
involved in aluminum resist structural genomics; HET:
MSE TLA PLP; 2.00A {Clostridium novyi} PDB: 3gwp_A*
Length = 427
Score = 25.9 bits (57), Expect = 7.8
Identities = 5/35 (14%), Positives = 10/35 (28%)
Query: 100 EKLEEDVARLHQKEAGLVFTSCYVANDSTLFTLGK 134
+ + V F + A + LF +
Sbjct: 79 DAVYARVFNTESALVRPHFVNGTHALGAALFGNLR 113
>3o9p_A Periplasmic murein peptide-binding protein; oligopeptide binding
proteins, murein tripeptide, periplasmi protein; HET:
MHI; 2.07A {Escherichia coli}
Length = 519
Score = 26.1 bits (58), Expect = 8.7
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 125 NDSTL-FTLGKMIPYFTELIYFYRFL 149
+ TL L K +P+F L + F
Sbjct: 144 DAHTLKIQLDKPLPWFVNLTANFAFF 169
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.134 0.389
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,717,344
Number of extensions: 153913
Number of successful extensions: 457
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 63
Length of query: 174
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 87
Effective length of database: 4,272,666
Effective search space: 371721942
Effective search space used: 371721942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.5 bits)